High‐throughput two‐dimensional root system phenotyping platform facilitates genetic analysis of root growth and development

Clark, Randy; Famoso, Adam N.; Zhao, Keyan; Shaff, Jon E.; Craft, Eric; Bustamante, Carlos D.; McCouch, Susan R.; Aneshansley, Daniel J.; Kochian, Leon V.

doi:10.1111/j.1365-3040.2012.02587.x

Cited by 194 publications

(146 citation statements)

References 45 publications

Supporting

Mentioning

144

Contrasting

Unclassified

Order By: Relevance

“…Highly relevant parameters for high-throughput phenotyping are computing time and, most importantly, the time required for user interaction. We therefore compared the performance of BRAT regarding these parameters with the popular published root analysis software tools EZ-Rhizo (Armengaud et al, 2009), RootTrace (French et al, 2009), SmartRoot (Lobet et al, 2011), and RootReader2D (Clark et al, 2013). We conducted this comparison in two common scenarios for quantitative large-scale data acquisition.…”

Section: Resultsmentioning

confidence: 99%

A Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis

et al. 2014

View full text Add to dashboard Cite

Large-scale phenotyping of multicellular organisms is one of the current challenges in biology. We present a comprehensive and scalable pipeline that allows for the efficient phenotyping of root growth traits on a large scale. This includes a highresolution, low-cost acquisition setup as well as the automated image processing software BRAT. We assess the performance of this pipeline in Arabidopsis thaliana under multiple growth conditions and show its utility by performing genome-wide association studies on 16 root growth traits quantified by BRAT each day during a 5-d time-course experiment. The most significantly associated genome region for root growth rate is a locus encoding a calcium sensing receptor. We find that loss of function and overexpression of this gene can significantly alter root growth in a growth condition dependent manner and that the minor natural allele of the Calcium Sensor Receptor locus is highly significantly enriched in populations in coastal areas, demonstrating the power of our approach to identify regulators of root growth that might have adaptive relevance.

show abstract

Section: Resultsmentioning

confidence: 99%

A Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis

et al. 2014

View full text Add to dashboard Cite

show abstract

“…Hence, the profile of branching density on firstorder LRs is determined by both their basal diameter and their elongation and may be an inherent feature of maize plants. Detailed root traits have been extracted mostly for seedling root systems, using recently developed automated/semi-automated methods in two or three dimensions (Iyer-Pascuzzi et al, 2010;Clark et al, 2011Clark et al, , 2012Mairhofer et al, 2012;Nagel et al, 2012;Tracy et al, 2012). These results, combined with root function studies, facilitate the parameterization of root architectural models used to simulate the whole root systems of young plants.…”

Section: Discussionmentioning

confidence: 99%

Relationships between root diameter, root length and root branching along lateral roots in adult, field-grown maize

Pagès

2016

Ann Bot

View full text Add to dashboard Cite

Background and Aims Root diameter, especially apical diameter, plays an important role in root development and function. The variation in diameter between roots, and along roots, affects root structure and thus the root system's overall foraging performance. However, the effect of diameter variation on root elongation, branching and topological connections has not been examined systematically in a population of high-order roots, nor along the roots, especially for mature plants grown in the field.Methods A method combining both excavation and analysis was applied to extract and quantify root architectural traits of adult, field-grown maize plants. The relationships between root diameter and other root architectural characteristics are analysed for two maize cultivars.Key Results The basal diameter of the lateral roots (orders 1-3) was highly variable. Basal diameter was partly determined by the diameter of the bearing segment. Basal diameter defined a potential root length, but the lengths of most roots fell far short of this. This was explained partly by differences in the pattern of diameter change along roots. Diameter tended to decrease along most roots, with the steepness of the gradient of decrease depending on basal diameter. The longest roots were those that maintained (or sometimes increased) their diameters during elongation. The branching density (cm -1 ) of laterals was also determined by the diameter of the bearing segment. However, the location of this bearing segment along the mother root was also involved -intermediate positions were associated with higher densities of laterals.Conclusions The method used here allows us to obtain very detailed records of the geometry and topology of a complex root system. Basal diameter and the pattern of diameter change along a root were associated with its final length. These relationships are especially useful in simulations of root elongation and branching in source-sink models.

show abstract

“…After 13 d, root images were captured with a digital photography setup and analyzed using both the RootReader2D program (Clark et al, 2013; http:// www.plantmineralnutrition.net/rr2d.php) as well as WinRHIZO (http:// www.regent.qc.ca/assets/winrhizo_about.html) software. The following root traits were measured as described by de Sousa et al (2012): total root length (designated root length; in cm), average root diameter (designated root diameter; in mm), volume of fine roots (diameter between 1 and 2 mm; in mm 3 ), and total root surface area (designated root surface area; in cm 2 ).…”

Section: Root Morphology Analysis In the Sapstmentioning

confidence: 99%

“…Broad sense heritabilities were high, with values of 0.63 for grain yield under low P in the SAPst and 0.42 and 0.59 for P content in single tillers and single tiller biomass, respectively, in the WAP. For assessing root morphology traits in a paper pouch system, our RootReader2D system (Clark et al, 2013) was used to process the root systems images and the WhinRhizo software was used to automatically calculate a number of root morphology traits including root length, root diameter, volume of fine roots and root surface area under low-P conditions (de Sousa et al 2012). Heritability estimates for the root morphology traits were high (h 2 .…”

Section: Phenotypic Characterization Of the Sorghum Association Panelsmentioning

confidence: 99%

Duplicate and Conquer: Multiple Homologs ofPHOSPHORUS-STARVATION TOLERANCE1Enhance Phosphorus Acquisition and Sorghum Performance on Low-Phosphorus Soils

et al. 2014

Self Cite

View full text Add to dashboard Cite

Low soil phosphorus (P) availability is a major constraint for crop production in tropical regions. The rice (Oryza sativa) protein kinase, PHOSPHORUS-STARVATION TOLERANCE1 (OsPSTOL1), was previously shown to enhance P acquisition and grain yield in rice under P deficiency. We investigated the role of homologs of OsPSTOL1 in sorghum (Sorghum bicolor) performance under low P. Association mapping was undertaken in two sorghum association panels phenotyped for P uptake, root system morphology and architecture in hydroponics and grain yield and biomass accumulation under low-P conditions, in Brazil and/or in Mali. Root length and root surface area were positively correlated with grain yield under low P in the soil, emphasizing the importance of P acquisition efficiency in sorghum adaptation to low-P availability. SbPSTOL1 alleles reducing root diameter were associated with enhanced P uptake under low P in hydroponics, whereas Sb03g006765 and Sb03g0031680 alleles increasing root surface area also increased grain yield in a low-P soil. SbPSTOL1 genes colocalized with quantitative trait loci for traits underlying root morphology and dry weight accumulation under low P via linkage mapping. Consistent allelic effects for enhanced sorghum performance under low P between association panels, including enhanced grain yield under low P in the soil in Brazil, point toward a relatively stable role for Sb03g006765 across genetic backgrounds and environmental conditions. This study indicates that multiple SbPSTOL1 genes have a more general role in the root system, not only enhancing root morphology traits but also changing root system architecture, which leads to grain yield gain under low-P availability in the soil.

show abstract

High‐throughput two‐dimensional root system phenotyping platform facilitates genetic analysis of root growth and development

Cited by 194 publications

References 45 publications

A Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis

A Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis

Relationships between root diameter, root length and root branching along lateral roots in adult, field-grown maize

Duplicate and Conquer: Multiple Homologs ofPHOSPHORUS-STARVATION TOLERANCE1Enhance Phosphorus Acquisition and Sorghum Performance on Low-Phosphorus Soils

Contact Info

Product

Resources

About